iNGNN-DTI:用可解释嵌套图形神经网络和预训练的分子模型预测药物向相互作用
Yan Sun1,2,3, Yan Yi Li4, Carson K Leung2
1Department of Biochemistry, Western University, London, ON, N6G 2V4, Canada.
Bioinformatics (Oxford, England)
|March 7, 2024
概括
我们开发了一个可解释的嵌套图形神经网络 (iNGNN-DTI),用于药物向相互作用的预测. 这种模型提高了预测准确度,并提供了对相互作用的洞察力,优于现有方法.
科学领域:
- 计算生物学 计算生物学
- 药物发现 药物发现 药物发现
- 生物信息学是一种生物信息学.
背景情况:
- 药物向相互作用 (DTI) 的预测对于药物发现至关重要.
- 用于DTI预测的深度学习模型在特征学习和可解释性方面面临挑战.
- 有限的标记数据可能会阻碍现有的DTI预测模型的泛化.
研究的目的:
- 为药物向相互作用预测 (iNGNN-DTI) 提出一个可解释的嵌套图形神经网络.
- 为了提高DTI预测的准确性,并提供有关底层相互作用的见解.
- 通过整合预先训练的分子和蛋白质特征来提高模型概括性.
主要方法:
- 使用嵌套图形神经网络架构与预训练的分子和蛋白质模型.
- 采用AlphaFold2用于图形构造的蛋白质标的纳入3D结构信息.
- 采用交叉注意模块来捕捉药物和目标之间的子结构相互作用.
- 集成的特征从模型预先训练在大型未标记的小分子和蛋白质数据集.
主要成果:
- 在三个基准数据集上,iNGNN-DTI模型表现出与基线模型相比的持续改进.
- 该模型在以前未见过的药物或目标上表现出卓越的性能,表明强烈的概括性.
- 交叉注意模块的学习权重为药物向相互作用提供了可解释的见解.
结论:
- 拟议的iNGNN-DTI为药物向相互作用的预测提供了一种有效和可解释的方法.
- 整合结构信息和预训练功能可以提高DTI预测性能和概括性.
- 可解释性功能有助于理解药物向相互作用的机制.
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